Effects of applying composted aquatic plants on soil chemistry, soil microbes (fungi and bacteria), and plant yield were demonstrated, and the relative importance of soil chemistry and microbes on the plant yield was examined to identify microbial drivers promoting plant yield on soil amended with composted aquatic plants. Experimental data of pot experiments were combined in structural equation models by hypothesizing causal relationships between the amendments, soil chemistry, soil microbes, and plant yields to explore significant pathways for the effects of composted aquatic plants, inorganic chemical fertilizer, or their mixtures on soil and plants. Plant yield, total carbon content in soil, and soil bacterial and fungal richness increased on soil amended with composted aquatic plants, and the compositions of bacterial and fungal assemblages in soil were significantly different depending on the treatments. Structural equation models explicitly demonstrated the relative importance of bacterial assemblages as a promoter of plant yield in response to the amendment of composted aquatic plants. To the knowledge of the authors, the present study is the first to detail the positive effect of composted aquatic plants on plant yield with reference to soil microbial and chemical changes.